NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|310703592|ref|NP_001185522|]
View 

STON1-GTF2A1L protein isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
AP_stonin-1_MHD cd09262
Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned ...
 403-716 0e+00

Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor); A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 1, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-1 is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin-1.


:

Pssm-ID: 271168  Cd Length: 314  Bit Score: 647.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  403 VSKPKKNYEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDLELPKRDESYYEKDSEKKGIDI 482
Cdd:cd09262     1 VSQPKRNYEEQELSLEIVDNFWGKVTKEGKVVESAVITQIYCLCFVNGPGECFLTLNDLELLKRDESYGEKEAGKKWIEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  483 LDYHFHKCVNVQEFEQSRIIKFVPLDACRFELMRFKTLYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSSYAGSL 562
Cdd:cd09262    81 LDCHFHKCVNEQEFEQSRIIKFSPLDACRAELMRFKTAYNGTQLPFSVKATVVVQGAYVELQAFLNMASTALSFGVSDSH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  563 RSCDNIRIHFPVPSQWIKALWTMNLQRQKSLKAKMNRRACLGSLQELESEPVIQVTVGSAKYESAYQAVVWKIDRLPDKN 642
Cdd:cd09262   161 PLCENVVIRFPVPAQWIKALWTMNLQRQKSLKAKMNRRACLGALRETESRPVIQVSVGTAKYESAYSAVVWKIDRLPDKN 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 310703592  643 SSLDHPHCLSYKLELGSDQEIPSDWYPFATVQFSVPDTCASRTEVRSLGVESDVQPQKHVQQRACYNIQPKLYR 716
Cdd:cd09262   241 SSLDHPHSLSYKLELGSDQEIPSDWYPFATVQFEVMDTCASQTEVKSLGTESDMQPQKHVTQWARYHCQAEFYK 314
TFIIA pfam03153
Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a ...
 714-1147 3.14e-60

Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.


:

Pssm-ID: 460829 [Multi-domain]  Cd Length: 344  Bit Score: 210.36  E-value: 3.14e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   714 LYRSVIEDVIEGVRNLFAEEGIEEQVLKDLKQLWETKVLQSKATE---DFFRNSIQSPLFTlqlphslhqtlqsstaslv 790
Cdd:pfam03153    1 VYRSVIEDVINASRVDFEEEGVDEQVLEELKQLWQSKLSQSKVAEfpwDPKPEPPHPPPFV------------------- 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   791 ipagrtlpsfttaelgtsnssanftfpgypIHVPAGVTLQTVSGHLYKVNVPimvTETSGRAGILQHPIQQVfqqlgQPS 870
Cdd:pfam03153   62 ------------------------------IKQEPGVTLQPASGPQAQLYKN---VQAQGAAQRAAQPLQQQ-----QGS 103

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   871 VIQTSVPQLNP---WSLQATTEKSQRI-------ETVLQQPAILPSGP-VDRKHLEnatsdilvspgnehkivPEALLCH 939
Cdd:pfam03153  104 AAQSSINALQAgasQQQQALALPQQQPqpqqqqqQQQQQQQQQQQQQQqQQQQQQE-----------------QAQQAPQ 166

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   940 QESSHyislpgvvfSPQVSQTNSNVESVLSGSASMAQNLHDESLSTS-PHGALHQHVTDIQLHI-----------LKNRM 1007
Cdd:pfam03153  167 QGGLN---------NSQTDGADDALEDWEGVLAQRRAAGAPEELGRVeIDRMLREQIAARAKQMggglmlplkeaLKGKS 237

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  1008 YGCDSVKQPRNIEepsnipvsekdsnsqvdlsirvtdddigEIIQVDGSGDTSSNEEigstrdadeneflgnidggdlkv 1087
Cdd:pfam03153  238 RAKKSRKAPRATA----------------------------EIAQLDGAGDDSDDEE----------------------- 266

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 310703592  1088 peeeadsISNEDSatnssdnedpqvnivEEDPLNSG-DDVSEQDVPDLFDTDN----VIVCQYDK 1147
Cdd:pfam03153  267 -------SSNEDD---------------DEDAINSDlDDPDDDDDDDLEDTDNalghVMLCQYDK 309
 
Name Accession Description Interval E-value
AP_stonin-1_MHD cd09262
Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned ...
 403-716 0e+00

Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor); A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 1, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-1 is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin-1.


Pssm-ID: 271168  Cd Length: 314  Bit Score: 647.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  403 VSKPKKNYEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDLELPKRDESYYEKDSEKKGIDI 482
Cdd:cd09262     1 VSQPKRNYEEQELSLEIVDNFWGKVTKEGKVVESAVITQIYCLCFVNGPGECFLTLNDLELLKRDESYGEKEAGKKWIEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  483 LDYHFHKCVNVQEFEQSRIIKFVPLDACRFELMRFKTLYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSSYAGSL 562
Cdd:cd09262    81 LDCHFHKCVNEQEFEQSRIIKFSPLDACRAELMRFKTAYNGTQLPFSVKATVVVQGAYVELQAFLNMASTALSFGVSDSH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  563 RSCDNIRIHFPVPSQWIKALWTMNLQRQKSLKAKMNRRACLGSLQELESEPVIQVTVGSAKYESAYQAVVWKIDRLPDKN 642
Cdd:cd09262   161 PLCENVVIRFPVPAQWIKALWTMNLQRQKSLKAKMNRRACLGALRETESRPVIQVSVGTAKYESAYSAVVWKIDRLPDKN 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 310703592  643 SSLDHPHCLSYKLELGSDQEIPSDWYPFATVQFSVPDTCASRTEVRSLGVESDVQPQKHVQQRACYNIQPKLYR 716
Cdd:cd09262   241 SSLDHPHSLSYKLELGSDQEIPSDWYPFATVQFEVMDTCASQTEVKSLGTESDMQPQKHVTQWARYHCQAEFYK 314
Adap_comp_sub pfam00928
Adaptor complexes medium subunit family; This family also contains members which are coatomer ...
 401-709 1.57e-67

Adaptor complexes medium subunit family; This family also contains members which are coatomer subunits.


Pssm-ID: 395742  Cd Length: 259  Bit Score: 227.96  E-value: 1.57e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   401 PAVSKPKKNYEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDLELPkrdesyyekdsekkgI 480
Cdd:pfam00928    1 VPWRPPGIKYKKNEVFLDVIERVSVIVDKDGGLLNSEVQGTIDLKCFLSGMPELRLGLNDKLLL---------------I 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   481 DILDYHFHKCVNVQEFEQSRIIKFVPLDAcRFELMRFKTLYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSSyag 560
Cdd:pfam00928   66 ELDDVSFHQCVNLDKFESERVISFIPPDG-EFELMRYRLSTNEVKLPFTVKPIVSVSGDEGRVEIEVKLRSDFPKKL--- 141

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   561 slrSCDNIRIHFPVPSQwikalwtmnlqrqkslkakmnrraclgslqelESEPVIQVTVGSAKYESAYQAVVWKIDRLPD 640
Cdd:pfam00928  142 ---TAENVVISIPVPKE--------------------------------ASSPVLRVSDGKAKYDPEENALEWSIKKIPG 186

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   641 KNSSLDHPhCLSYKLELGSDQEIPSDWYpfATVQFSVPDTCASRTEVRSLGV-ESDVQPQKHVQQRACYN 709
Cdd:pfam00928  187 GNESSLSG-ELELSVESSSDDEFPSDPP--ISVEFSIPMFTASGLKVRYLKVeEENYKPYKWVRYVTQSG 253
TFIIA pfam03153
Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a ...
 714-1147 3.14e-60

Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.


Pssm-ID: 460829 [Multi-domain]  Cd Length: 344  Bit Score: 210.36  E-value: 3.14e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   714 LYRSVIEDVIEGVRNLFAEEGIEEQVLKDLKQLWETKVLQSKATE---DFFRNSIQSPLFTlqlphslhqtlqsstaslv 790
Cdd:pfam03153    1 VYRSVIEDVINASRVDFEEEGVDEQVLEELKQLWQSKLSQSKVAEfpwDPKPEPPHPPPFV------------------- 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   791 ipagrtlpsfttaelgtsnssanftfpgypIHVPAGVTLQTVSGHLYKVNVPimvTETSGRAGILQHPIQQVfqqlgQPS 870
Cdd:pfam03153   62 ------------------------------IKQEPGVTLQPASGPQAQLYKN---VQAQGAAQRAAQPLQQQ-----QGS 103

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   871 VIQTSVPQLNP---WSLQATTEKSQRI-------ETVLQQPAILPSGP-VDRKHLEnatsdilvspgnehkivPEALLCH 939
Cdd:pfam03153  104 AAQSSINALQAgasQQQQALALPQQQPqpqqqqqQQQQQQQQQQQQQQqQQQQQQE-----------------QAQQAPQ 166

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   940 QESSHyislpgvvfSPQVSQTNSNVESVLSGSASMAQNLHDESLSTS-PHGALHQHVTDIQLHI-----------LKNRM 1007
Cdd:pfam03153  167 QGGLN---------NSQTDGADDALEDWEGVLAQRRAAGAPEELGRVeIDRMLREQIAARAKQMggglmlplkeaLKGKS 237

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  1008 YGCDSVKQPRNIEepsnipvsekdsnsqvdlsirvtdddigEIIQVDGSGDTSSNEEigstrdadeneflgnidggdlkv 1087
Cdd:pfam03153  238 RAKKSRKAPRATA----------------------------EIAQLDGAGDDSDDEE----------------------- 266

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 310703592  1088 peeeadsISNEDSatnssdnedpqvnivEEDPLNSG-DDVSEQDVPDLFDTDN----VIVCQYDK 1147
Cdd:pfam03153  267 -------SSNEDD---------------DEDAINSDlDDPDDDDDDDLEDTDNalghVMLCQYDK 309
TFIIA_alpha_beta_like cd07976
Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A ...
 712-760 8.39e-20

Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage).


Pssm-ID: 199899 [Multi-domain]  Cd Length: 102  Bit Score: 85.65  E-value: 8.39e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 310703592  712 PKLYRSVIEDVIEGVRNLFAEEGIEEQVLKDLKQLWETKVLQSKATEDF 760
Cdd:cd07976     2 SKVYESVIEDVINNVREDFEDEGVDESVLQELKQLWEEKLSQSGAASFP 50
TOA1 COG5149
Transcription initiation factor IIA, large chain [Transcription];
713-819 3.52e-07

Transcription initiation factor IIA, large chain [Transcription];


Pssm-ID: 227478 [Multi-domain]  Cd Length: 293  Bit Score: 53.14  E-value: 3.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  713 KLYRSVIEDVIEGVRNLFAEEGIEEQVLKDLKQLWETKVLQSKATEDFFRNsiqsplftlQLPHSLHQTLQSSTASLVIP 792
Cdd:COG5149     8 EVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDVATFPWAQ---------AFPIGQLFGLRTDSLDVTAP 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 310703592  793 AGRTLPSFTTAELGTS---------NSSANFTFPGY 819
Cdd:COG5149    79 AVANSPILNQSATNISfdssaipnvQSNNTAPFPSY 114
 
Name Accession Description Interval E-value
AP_stonin-1_MHD cd09262
Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned ...
 403-716 0e+00

Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor); A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 1, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-1 is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin-1.


Pssm-ID: 271168  Cd Length: 314  Bit Score: 647.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  403 VSKPKKNYEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDLELPKRDESYYEKDSEKKGIDI 482
Cdd:cd09262     1 VSQPKRNYEEQELSLEIVDNFWGKVTKEGKVVESAVITQIYCLCFVNGPGECFLTLNDLELLKRDESYGEKEAGKKWIEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  483 LDYHFHKCVNVQEFEQSRIIKFVPLDACRFELMRFKTLYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSSYAGSL 562
Cdd:cd09262    81 LDCHFHKCVNEQEFEQSRIIKFSPLDACRAELMRFKTAYNGTQLPFSVKATVVVQGAYVELQAFLNMASTALSFGVSDSH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  563 RSCDNIRIHFPVPSQWIKALWTMNLQRQKSLKAKMNRRACLGSLQELESEPVIQVTVGSAKYESAYQAVVWKIDRLPDKN 642
Cdd:cd09262   161 PLCENVVIRFPVPAQWIKALWTMNLQRQKSLKAKMNRRACLGALRETESRPVIQVSVGTAKYESAYSAVVWKIDRLPDKN 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 310703592  643 SSLDHPHCLSYKLELGSDQEIPSDWYPFATVQFSVPDTCASRTEVRSLGVESDVQPQKHVQQRACYNIQPKLYR 716
Cdd:cd09262   241 SSLDHPHSLSYKLELGSDQEIPSDWYPFATVQFEVMDTCASQTEVKSLGTESDMQPQKHVTQWARYHCQAEFYK 314
AP-like_stonins_MHD cd09255
Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of ...
 403-711 1.82e-166

Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonins, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonins is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin 1. Stonin 2, also known as stoned B, acts as an AP-2-dependent synaptotagmin-specific sorting adaptors for SV endocytosis. Stoned A is not a stonin. It is structurally unrelated to the adaptins and does not appear to have mammalian homologs. It is not included in this family.


Pssm-ID: 271163 [Multi-domain]  Cd Length: 315  Bit Score: 494.62  E-value: 1.82e-166
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  403 VSKPKKNYEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDLELPKRDES---YYEKDSEKKG 479
Cdd:cd09255     1 YRDRGITYREDEITVDVTDEFHGKVTKTGEIKKLGVTVQIHILSFVTGDPECVLGLNDLEVEGREVVrrqDIMPSSTDQW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  480 IDILDYHFHKCVNVQEFEQSRIIKFVPLDACRFELMRFKTLYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSsyA 559
Cdd:cd09255    81 IKLHNCEFHSCVDVEEFEQSRSIKFHPLDACRFELMRFRTRYNKKNLPLTLKSVVSVKGAHVELRADVRMSGYHSRN--P 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  560 GSLRSCDNIRIHFPVPSQWIKALWTMNLQRQKSLKAKMNRRACLGSLQELESEPVIQVTVGSAKYESAYQAVVWKIDRLP 639
Cdd:cd09255   159 LAQVPCENIMIRFPVPESWVPAFRTEKRFREKSLKSKKNKKASGGSTAESLSEPVIEVSVGSAKYEHAYRAVVWRIDRLP 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 310703592  640 DKNSSLDHPHCLSYKLELGSDQEIPSDWYPFATVQFSVPDTCASRTEVRSLGVESDVQPQKHVQQRACYNIQ 711
Cdd:cd09255   239 DKNSAADTPHTFSCRLDLASDLEIPSSTYPHAEVEFTMPSTTASKTTVRSISVSNKNIPEKWVRYRAHYSYK 310
AP_stonin-2_MHD cd09263
Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-2; A small family of ...
 409-711 7.74e-85

Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-2; A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 2, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-2 is unable to recognize tyrosine-based endocytic sorting signals. It acts as an AP-2-dependent synaptotagmin-specific sorting adaptor for SV endocytosis.


Pssm-ID: 271169  Cd Length: 318  Bit Score: 278.44  E-value: 7.74e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  409 NYEEQEISLEIVDNFWGKVTK-EGKFVESAVITQIYCLCFVNGNLECFLTLNDLELpKRDESYYEKD----SEKKGIDIL 483
Cdd:cd09263     7 NYTEEEITVDVRDEFYGILSKgDSRILQHLVLTRINMLSFLSGLAECRLGLNDILI-KGNEIVSRQDimptTTTKWIKLR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  484 DYHFHKCVNVQEFEQSRIIKFVPLDACRFELMRFKTLYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSSYAGSLR 563
Cdd:cd09263    86 DCRFHECVDEDEFNNSRAILFNPLDACRFELMRFRTVFAEKTLPFTLRTAASVNGAEVEVQSWLVMSTGFSSNRDPLTQV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  564 SCDNIRIHFPVPSQWIKALWTMNLQRQKSLKAKMNRRACLGSLQELESEPVIQVTVGSAKYESAYQAVVWKIDRLPDKNS 643
Cdd:cd09263   166 PCENVMIRYPVPEEWVKNFRRESVLGEKSLKAKVNKGASFGSTSTSGSEPVMRVTLGTAKYEHAFNSIVWRINRLPDKNS 245

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 310703592  644 SLDHPHCLSYKLELGSDQEIPSDWYPFATVQFSVPDTCASRTEVRSLGVESDVQPQKHVQQRACYNIQ 711
Cdd:cd09263   246 ASGHPHCFFCHLELGSDREVPSTFECHVEVEFDMPTTSASKAAVRSISVEDKTDVRKWVNYSAHYSYQ 313
Adap_comp_sub pfam00928
Adaptor complexes medium subunit family; This family also contains members which are coatomer ...
 401-709 1.57e-67

Adaptor complexes medium subunit family; This family also contains members which are coatomer subunits.


Pssm-ID: 395742  Cd Length: 259  Bit Score: 227.96  E-value: 1.57e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   401 PAVSKPKKNYEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDLELPkrdesyyekdsekkgI 480
Cdd:pfam00928    1 VPWRPPGIKYKKNEVFLDVIERVSVIVDKDGGLLNSEVQGTIDLKCFLSGMPELRLGLNDKLLL---------------I 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   481 DILDYHFHKCVNVQEFEQSRIIKFVPLDAcRFELMRFKTLYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSSyag 560
Cdd:pfam00928   66 ELDDVSFHQCVNLDKFESERVISFIPPDG-EFELMRYRLSTNEVKLPFTVKPIVSVSGDEGRVEIEVKLRSDFPKKL--- 141

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   561 slrSCDNIRIHFPVPSQwikalwtmnlqrqkslkakmnrraclgslqelESEPVIQVTVGSAKYESAYQAVVWKIDRLPD 640
Cdd:pfam00928  142 ---TAENVVISIPVPKE--------------------------------ASSPVLRVSDGKAKYDPEENALEWSIKKIPG 186

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   641 KNSSLDHPhCLSYKLELGSDQEIPSDWYpfATVQFSVPDTCASRTEVRSLGV-ESDVQPQKHVQQRACYN 709
Cdd:pfam00928  187 GNESSLSG-ELELSVESSSDDEFPSDPP--ISVEFSIPMFTASGLKVRYLKVeEENYKPYKWVRYVTQSG 253
TFIIA pfam03153
Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a ...
 714-1147 3.14e-60

Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.


Pssm-ID: 460829 [Multi-domain]  Cd Length: 344  Bit Score: 210.36  E-value: 3.14e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   714 LYRSVIEDVIEGVRNLFAEEGIEEQVLKDLKQLWETKVLQSKATE---DFFRNSIQSPLFTlqlphslhqtlqsstaslv 790
Cdd:pfam03153    1 VYRSVIEDVINASRVDFEEEGVDEQVLEELKQLWQSKLSQSKVAEfpwDPKPEPPHPPPFV------------------- 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   791 ipagrtlpsfttaelgtsnssanftfpgypIHVPAGVTLQTVSGHLYKVNVPimvTETSGRAGILQHPIQQVfqqlgQPS 870
Cdd:pfam03153   62 ------------------------------IKQEPGVTLQPASGPQAQLYKN---VQAQGAAQRAAQPLQQQ-----QGS 103

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   871 VIQTSVPQLNP---WSLQATTEKSQRI-------ETVLQQPAILPSGP-VDRKHLEnatsdilvspgnehkivPEALLCH 939
Cdd:pfam03153  104 AAQSSINALQAgasQQQQALALPQQQPqpqqqqqQQQQQQQQQQQQQQqQQQQQQE-----------------QAQQAPQ 166

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592   940 QESSHyislpgvvfSPQVSQTNSNVESVLSGSASMAQNLHDESLSTS-PHGALHQHVTDIQLHI-----------LKNRM 1007
Cdd:pfam03153  167 QGGLN---------NSQTDGADDALEDWEGVLAQRRAAGAPEELGRVeIDRMLREQIAARAKQMggglmlplkeaLKGKS 237

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  1008 YGCDSVKQPRNIEepsnipvsekdsnsqvdlsirvtdddigEIIQVDGSGDTSSNEEigstrdadeneflgnidggdlkv 1087
Cdd:pfam03153  238 RAKKSRKAPRATA----------------------------EIAQLDGAGDDSDDEE----------------------- 266

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 310703592  1088 peeeadsISNEDSatnssdnedpqvnivEEDPLNSG-DDVSEQDVPDLFDTDN----VIVCQYDK 1147
Cdd:pfam03153  267 -------SSNEDD---------------DEDAINSDlDDPDDDDDDDLEDTDNalghVMLCQYDK 309
AP_MHD_Cterm cd07954
C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); ...
 414-693 8.91e-30

C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15.


Pssm-ID: 271157  Cd Length: 245  Bit Score: 119.05  E-value: 8.91e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  414 EISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDlelpkrdesyyeKDSEKKGIDILdyhFHKCVNV 493
Cdd:cd07954     1 EVFLDVVEKVNLLISKDGSLLNSEVQGEIALKSFLSGMPEIRLGLNN------------PDVGIKLDDVS---FHPCVRL 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  494 QEFEQSRIIKFVPLDaCRFELMRFKTLYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQrssyagslRSCDNIRIHFP 573
Cdd:cd07954    66 KRFESERVISFIPPD-GEFELMSYRTVEPWSILPITIFPVVSEEGSQLEVVITLKLSESLQ--------LTAENVEVHIP 136

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  574 VPSqwikalwtmnlqRQKSLKAKmnrraclgslqelesepviqVTVGSAKYESAYQAVVWKIDRLPDKNssldHPHCLSY 653
Cdd:cd07954   137 LPS------------GVTSLKSK--------------------PSDGQAKFDPEKNALVWRIKRIPVGG----KEQSLSA 180

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 310703592  654 KLELGSDQEIPSDWYPFATVQFSVPDTCASRTEVRSLGVE 693
Cdd:cd07954   181 HVELGSLAHECPEEAPPVSVSFEIPETTGSGIQVRSLQVF 220
AP-2_Mu2_Cterm cd09251
C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor ...
 407-692 3.92e-25

C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-2; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, -2, -3, and -4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 2 (AP-2) medium mu2 subunit. Mu2 is ubiquitously expressed in mammals. In higher eukaryotes, AP-2 plays a critical role in clathrin-mediated endocytosis from the plasma membrane in different cells. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-2. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-2 mu2 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Since the Y-X-X-Phi binding site is buried in the core structure of AP-2, a phosphorylation induced conformational change is required when the cargo molecules binds to AP-2. In addition, the C-terminal domain of mu2 subunit has been shown to bind other molecules. For instance, it can bind phosphoinositides, in particular PI[4,5]P2, which might be involved in the recognition process of the tyrosine-based signals. It can also interact with synaptotagmins, a family of important modulators of calcium-dependent neurosecretion within the synaptic vesicle (SV) membrane. Since many of the other endocytic adaptors responsible for biogenesis of synaptic vesicles exist, in the absence of AP-2, clathrin-mediated endocytosis can still occur. However, the cells may not survive in the complete absence of clathrin as well as AP-2.


Pssm-ID: 271159  Cd Length: 263  Bit Score: 106.14  E-value: 3.92e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  407 KKNyeeqEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLND-LELPKRDESYYEKDSEKKGIDILDY 485
Cdd:cd09251     2 RKN----EVFLDVVESVNLLMSPQGQVLRADVDGVIVMKTYLSGMPECKFGLNDkLVLESEGKEKSGSKSGKGSVELDDC 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  486 HFHKCVNVQEFEQSRIIKFVPLDAcRFELMRFKTLYNGdNLPFSLKSVVVVQGAyVELQAFVNMaslaqRSSYAGSLrSC 565
Cdd:cd09251    78 TFHQCVRLSKFDSERSISFIPPDG-EFELMRYRVTENI-NLPFRVIPLVKEVGR-TKLEYKVKI-----KSNFPPKL-LA 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  566 DNIRIHFPVPSQWIKAlwtmnlqrqkslkakmnrraclgslqelesepVIQVTVGSAKYESAYQAVVWKIDRLPDKNSsl 645
Cdd:cd09251   149 TNVVVRIPVPKNTAKV--------------------------------TINVSKGKAKYDPEENAIVWKIKKFAGMTE-- 194

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 310703592  646 dhpHCLSYKLELGSDQEIPSDWY-PFATVQFSVPDTCASRTEVRSLGV 692
Cdd:cd09251   195 ---STLSAEVELLSTTSKKKKWSrPPISMDFEVPMFTASGLRVRYLKV 239
TFIIA_alpha_beta_like cd07976
Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A ...
 712-760 8.39e-20

Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage).


Pssm-ID: 199899 [Multi-domain]  Cd Length: 102  Bit Score: 85.65  E-value: 8.39e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 310703592  712 PKLYRSVIEDVIEGVRNLFAEEGIEEQVLKDLKQLWETKVLQSKATEDF 760
Cdd:cd07976     2 SKVYESVIEDVINNVREDFEDEGVDESVLQELKQLWEEKLSQSGAASFP 50
AP-1_Mu1_Cterm cd09250
C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex ...
 407-699 3.75e-16

C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1 subunit, which includes two closely related homologs, mu1A (encoded by ap1m1) and mu1B (encoded by ap1m2). Mu1A is ubiquitously expressed, but mu1B is expressed exclusively in polarized epithelial cells. AP-1 has been implicated in bi-directional transport between the trans-Golgi network (TGN) and endosomes. It plays an essential role in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Epithelial cell-specific AP-1 is also involved in sorting to the basolateral surface of polarized epithelial cells. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding.


Pssm-ID: 271158  Cd Length: 272  Bit Score: 79.95  E-value: 3.75e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  407 KKNyeeqEISLEIVD--NFWgkVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDLELPKRdesyYEKDSEKKGIDILD 484
Cdd:cd09250    14 KKN----EVFLDVIEsvNLL--VDLNGQVLRSEIVGAIKMRSYLSGMPELKLGLNDKVLFEA----TGRSSKGKAVELED 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  485 YHFHKCVNVQEFEQSRIIKFVPLDAcRFELMRFKTLYNgDNLPFSLKSVVVVQGAY-VELqafvnMASLaqRSSYAGSLr 563
Cdd:cd09250    84 VKFHQCVRLSRFENDRTISFIPPDG-EFELMSYRLSTQ-VKPLIWVEPTVERHSRSrVEI-----MVKA--KTQFKRRS- 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  564 SCDNIRIHFPVPSqwikalwtmnlqrqkslkakmnrraclgslqeLESEPVIQVTVGSAKYESAYQAVVWKIDRLPDKNS 643
Cdd:cd09250   154 TANNVEIRIPVPP--------------------------------DADSPRFKCSAGSVVYAPEKDALLWKIKSFPGGKE 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 310703592  644 SLdhphcLSYKLELGS---DQEIPSDWYPFATVQFSVPDTCASRTEVRSLGVESDVQPQ 699
Cdd:cd09250   202 FS-----MRAEFGLPSiesEEEQGTEKKAPIQVKFEIPYFTVSGLQVRYLKIIEKSGYQ 255
AP-3_Mu3_Cterm cd09252
C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3; AP complexes ...
 405-702 6.83e-15

C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3 subunit, which includes two closely related homologs, mu3A (P47A, encoded by ap3m1) and mu1B (P47B, encoded by ap3m2). Mu3A is ubiquitously expressed, but mu3B is specifically expressed in neurons and neuroendocrine cells. AP-3 is particularly important for targeting integral membrane proteins to lysosomes and lysome-related organelles at trans-Golgi network (TGN) and/or endosomes, such as the yeast vacuole, fly pigment granules and mammalian melanosomes, platelet dense bodies and the secretory lysosomes of cytotoxic T lymphocytes. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding.


Pssm-ID: 271160  Cd Length: 251  Bit Score: 75.70  E-value: 6.83e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  405 KPKKNYEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLNDlelpkrdesyyekdsekkGIDILD 484
Cdd:cd09252     5 RAGVKYTNNEIYFDVVEEIDAIVDKSGKPVSGEVRGEIDCNSRLSGMPDLLLSFNN------------------PRLLDD 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  485 YHFHKCVNVQEFEQSRIIKFVPLDAcRFELMRFK-TLYNGDNLPFSLKSVVVVQGAYVELQAFVNMaslaqRSSYAGSLr 563
Cdd:cd09252    67 PSFHPCVRYSRWESERVLSFIPPDG-KFTLMSYRvDLNSLVSLPVYVKPQISFSGSSGRFEITVGS-----RQNLGKSI- 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  564 scDNIRIHFPVPSqwikalwtmnlqrqkslKAKMNRRAclgslqelesepviqVTVGSAKYESAYQAVVWKIDRL-PDKN 642
Cdd:cd09252   140 --ENVVVEIPLPK-----------------GVKSLRLT---------------ASHGSFSFDSSTKTLVWNIGKLtPGKT 185

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 310703592  643 SsldhphCLSYKLELGSDQEIPSDwYPFATVQFSVPDTCASRTEVRSLGVES-DVQPQKHV 702
Cdd:cd09252   186 P------TLRGSVSLSSGLEAPSE-SPSISVQFKIPGYTPSGLKVDSLDIYNeKYKPFKGV 239
AP-1_Mu1B_Cterm cd09259
C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated ...
 410-692 2.70e-14

C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1B subunit encoded by ap1m2 gene exclusively expressed in polarized epithelial cells. Epithelial cell-specific AP-1 is used to sort proteins to the basolateral plasma membrane, which involves the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). The phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1B subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic reside-binding. Besides, AP-1 mu1B subunit mediates the basolateral recycling of low-density lipoprotein receptor (LDLR) and transferrin receptor (TfR) from the sorting endosomes, where the basolateral sorting signal does not belong to the tyrosine-based signals. Thus, the binding site in mu1B subunit of AP-1 for the signals of LDLR and TfR might be distinct from that for YXXPhi signals.


Pssm-ID: 271167  Cd Length: 268  Bit Score: 74.29  E-value: 2.70e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  410 YEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLND---LELPKRDESyyekdsekKGIDILDYH 486
Cdd:cd09259    13 YKKNEVFIDVIESVNVLVNANGSVLSSEIVGCIKLKVFLSGMPELRLGLNDrvlFELTGRDKN--------KTVELEDVK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  487 FHKCVNVQEFEQSRIIKFVPLDAcRFELMRFKTlyNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSSYAgslrscD 566
Cdd:cd09259    85 FHQCVRLSRFENDRTISFIPPDG-DFELMSYRL--NTQVKPLIWIESVIEKFSHSRVEIMVKAKGQFKKQSVA------N 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  567 NIRIHFPVPSQwikalwtmnlqrqkslkakmnrraclgslqelESEPVIQVTVGSAKYESAYQAVVWKIDRLPDKNSSLD 646
Cdd:cd09259   156 NVEIRVPVPSD--------------------------------ADSPKFKTSVGSAKYVPEKNVVVWSIKSFPGGKEYLM 203

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 310703592  647 HPHclsYKLELGSDQEIPSDwyPFATVQFSVPDTCASRTEVRSLGV 692
Cdd:cd09259   204 RAH---FGLPSVENEELEGK--PPITVKFEIPYFTVSGIQVRYMKI 244
AP-1_Mu1A_Cterm cd09258
C-terminal domain of medium Mu1A subunit in ubiquitously expressed clathrin-associated adaptor ...
 410-692 5.20e-13

C-terminal domain of medium Mu1A subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1A subunit encoded by ap1m1 gene, which is ubiquitously expressed in all mammalian tissues and cells. AP-1 has been implicated in bidirectional transport between the trans-Golgi network (TGN) and endosomes. It is involved in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). The ubiquitous AP-1 is recruited to the TGN membrane, as well as to immature secretory granules. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1A subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding.


Pssm-ID: 271166  Cd Length: 270  Bit Score: 70.68  E-value: 5.20e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  410 YEEQEISLEIVDNFWGKVTKEGKFVESAVITQIYCLCFVNGNLECFLTLND---LELPKRDESyyekdsekKGIDILDYH 486
Cdd:cd09258    14 YRKNEVFLDVIESVNLLVSANGNVLRSEIVGSIKMRVYLSGMPELRLGLNDkvlFENTGRGKS--------KSVELEDVK 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  487 FHKCVNVQEFEQSRIIKFVPLDAcRFELMRFKtlYNGDNLPFSLKSVVVVQGAYVELQAFVNMASLAQRSSYAgslrscD 566
Cdd:cd09258    86 FHQCVRLSRFENDRTISFIPPDG-EFELMSYR--LNTHVKPLIWIESVIERHSHSRVEYMIKAKSQFKRRSTA------N 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  567 NIRIHFPVPSQwikalwtmnlqrqkslkakmnrraclgslqelESEPVIQVTVGSAKYESAYQAVVWKIDRLPDKNSSLD 646
Cdd:cd09258   157 NVEIHIPVPND--------------------------------ADSPKFKTTVGSVKYVPENSEIVWSIKSFPGGKEYLM 204

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 310703592  647 HPHclsykLELGSDQEIPSDWYPFATVQFSVPDTCASRTEVRSLGV 692
Cdd:cd09258   205 RAH-----FGLPSVESEEKEGRPPISVKFEIPYFTTSGIQVRYLKI 245
AP-4_Mu4_Cterm cd09253
C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4; AP complexes ...
 446-695 6.46e-12

C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 4 (AP-4) medium mu4 subunit. AP-4 plays a role in signal-mediated trafficking of integral membrane proteins in mammalian cells. Unlike other AP complexes, AP-4 is found only in mammals and plants. It is believed to be part of a nonclathrin coat, since it might function independently of clathrin, a scaffolding protein participating in the formation of coated vesicles. Recruitment of AP-4 to the trans-Golgi network (TGN) membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1) or a related protein. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. One of the most important sorting signals binding to mu subunits of AP complexes are tyrosine-based endocytotic signals, which are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. However, AP-4 does not bind most canonical tyrosine-based signals except for two naturally occurring ones from the lysosomal membrane proteins CD63 and LAMP-2a. It binds YX [FYL][FL]E motif, where X can be any residue, from the cytosolic tails of amyloid precursor protein (APP) family members in a distinct way.


Pssm-ID: 271161  Cd Length: 271  Bit Score: 67.21  E-value: 6.46e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  446 CFVNGNLECFLTLN-DLELPKRDESYYEkdsekkGIDILDY-HFHKCVNVQEFEQSRIIKFVPLDAcRFELMRFKtLYNG 523
Cdd:cd09253    44 SYLPGNPELRLALNeDLVIGKRENRAYY------SAVVLDDcNFHESVDLEEFESDRTLSLTPPDG-EFTLMNYR-ISGE 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  524 DNLPFSLKSVVVVQGAY---VELQAFVNMASlaqrSSYagslrsCDNIRIHFPVPSqwikalWTMNLQrqkslkakmnrr 600
Cdd:cd09253   116 FKPPFRVFPSVEETSPYkleLVLKLRADFPP----KST------ATNVVVRIPLPK------GTTSVS------------ 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  601 aclgslQELESEPVIQvtvgSAKYESAYQAVVWKIDRLPDKnssldHPHCLSYKLELGS--DQEIPSDWYPfATVQFSVP 678
Cdd:cd09253   168 ------CELGSGASGQ----SAEYKEKEKLVLWNIKKFPGG-----TELTLRAKITLSSpvSSSVRKEIGP-ISLSFEIP 231

                         250
                  ....*....|....*..
gi 310703592  679 DTCASRTEVRSLGVESD 695
Cdd:cd09253   232 MYNVSGLQVRYLRILER 248
TOA1 COG5149
Transcription initiation factor IIA, large chain [Transcription];
713-819 3.52e-07

Transcription initiation factor IIA, large chain [Transcription];


Pssm-ID: 227478 [Multi-domain]  Cd Length: 293  Bit Score: 53.14  E-value: 3.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 310703592  713 KLYRSVIEDVIEGVRNLFAEEGIEEQVLKDLKQLWETKVLQSKATEDFFRNsiqsplftlQLPHSLHQTLQSSTASLVIP 792
Cdd:COG5149     8 EVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDVATFPWAQ---------AFPIGQLFGLRTDSLDVTAP 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 310703592  793 AGRTLPSFTTAELGTS---------NSSANFTFPGY 819
Cdd:COG5149    79 AVANSPILNQSATNISfdssaipnvQSNNTAPFPSY 114
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH